[MNT] `pre-commit` updates

[satvshr]

We should update the pre-commit versions of the repository with the latest versions supported by pre-commit. Currently in pre-commit we face some problems:

1. Mypy checks are ignoring the entire tests repository, same with ruff.
2. Upgrading the mypy version from 1.13.0 to the most recent stable version 1.19.1 results in failures as observed in [MNT] Update ruff and mypy versions #1637.

cc: @fkiraly @PGijsbers